The match's first real chance fell for Stars in the 10th minute when Nomandela broke loose on the leftwing and sent in a low cross for Henyekane whose effort was blocked goalkeeper Moeneeb Josephs.
In the 15th minute, Siyabonga Nhlapo played a beautiful cross for Sibusiso Vilakazi who was unmarked inside the box but the Wits skipper rifled the ball over the cross.
Nomandela's pace continued to trouble the Wits defence and again it came in handy in the 22nd minute as he outpaced a defender then set up Angelo Kerspuy who disappointingly fired over the bar.
In the 34th minute, Jabulani Shongwe pulled the trigger on the edge of the Stars box but his venomous shot went over the bar.
Stars responded with a quick counter attack and Henyekane capitalised on some poor defending by Wits to beat Josephs with a sublime finish in the 37th minute.
In second half the Clever Boys came out firing in all cylinders and nearly leveled matters in the 47th minute.
Ryan Chapman found himself unmarked on the edge of the box but his pile driver was parried out by goalkeeper Tshepo Motsoeneng.
Stars coach Kinnah Phiri was forced to rethink his tactics as goalkeeper Motsoeneng was stretchered off with a pulled hamstring and had to be replaced by Ayanda Mtshali on the hour mark.
In the 70th minute, Nomandela beat the offside trap and unselfishly laid the ball for Henyekane to double the Stars lead with a cool finish.
Wits had a chance to pull one back in the 75th minute but Papy Faty's grass cutter missed the upright with keeper Mtshali seemingly beaten.
In the 86th minute, Wits were reduced to ten men after Tebogo Moerane was sent off for a second bookable offence.
Stars took advantage of an extra man on the pitch as Henyekane beat Josephs for the third time in the 87th minute.
Substitute Robin Ngalande pulled one back for Wits in the 90th minute but it was already too late, Henyekane had already done the damage.
The loss means Wits are now six points off runaway leaders Kaizer Chiefs while the win for Stars mean they move from 15th to 13th position. Sapa